Rapture
by TaroStrike
Summary: Red and Giovanni wage an epic dual. By winning Red hopes to dissolve Team Rocket forever while Giovanni is determined to open Red's eyes to the truth to see the world as he does. Adventures Manga.
1. Viridian Providence

Pokémon

Rapture

(Valentine Reboot)

Disclaimer:

-The author does not own any part of the Pokémon series, including but not limited to the characters of the story.

-This story is entirely fictional, based from purely fictional premise, none of the characters, actions characters partake in, many contraptions found here-in did not happen/do not actually exist.

-No money was made from the creation or distribution of this fic.

-No animals/people/Pokémon were hurt in the making of this fic.

-The author does not encourage nor endorse others to partake in actions as described within the story.

Warnings:

This story is rated M(Mature)+ for the following reasons:

-Extreme Violence

-Situations of Angst

-Explicit depictions of kidnapping, murder, torture, and rape

-Explicit depictions of sexual acts including sexual involvement of minors

If any of these themes offend you, please do not continue to read this story.

Notes:

I can hardly believe I'm doing this myself. I have wanted to finish this story for so long, and after years of it sitting here I finally was hit by the inspiration to try again. I'm not positive yet I'll carry drive through to the end as this story has had enough time in my mind to become extremely fleshed out. The good thing about that is I have a much more definite path that I want this story to follow, or at least a series of events that need to happen somehow.

This is not going to be a kid friendly story. This story is violent and gruesome and deals with horrible themes. I see this version of Pokémon as gritty and almost hyper realistic. Good people will be hurt and bad things will happen followed by even worse things. If you're up for it then I welcome you to the new Rapture.

* * *

 **Chapter 1: Viridian Providence**

* * *

It was cold in the Viridian City gym. An icy prickling tickled at Red's skin as he pushed himself to his feet. A groan to his right caused him to quickly shake off the haze in his head, but it didn't clear the icy haze in the room, "Poli!" The young trainer ran to his downed Poliwrath's side. A frostbite like burn marred the side of the huge fighting frog Pokémon.

"It's a shame Red…" Red shot to his feet as the voice approached through the fog; the voice of Team Rocket's leader, the mysterious Giovanni, "It really is…"

Red stepped forward angrily towards the man, "What are you callin'…"

Giovanni put up a hand to interrupt the boy, "Don't misunderstand me… There was nothing shameful about your attack. The shame is that you're not on my side. I could use a trainer with your stubbornness, your explosive energy, your empathy with Pokémon."

In an even greater flood of anger, Red waved his hand to the side, "YOU THINK I'D JOIN YOU?!"

The fog in the room felt thicker as a sullen look crossed Giovanni's face as his gaze downturned, "No actually… I don't. You see your independence and honor are among the traits I admire in you." Giovanni began pacing around the trainer as the two appraised each other for the next move, "So then… how about a bet?"

Unsure what the Rocket boss was getting at, Red took a step back apprehensively. He watched carefully as Giovanni pulled his Poké Balls from his belt and tossed them all to the ground in front of him, "As you can see my Pokémon are on the floor far from me." Giovanni turned and took a few precise steps away before turning back, "It will take six seconds for me to seize one and attack. On the other hand you have five Pokémon still at your side."

Red reached for his Poké Balls almost subconsciously as if to confirm the statement but continued to watch the scene play out, "If you can win under these conditions I'll make no demands on you. I'll accept whatever you decide… However if I win…" a look of grim seriousness crossed Giovanni's eyes as the two combatants stared through each other's souls, "If I win you will spend the rest of your life battling for ME at my side! Well?"

A chilled breath escaped Red's mouth as he contemplated Giovanni's offer. One victory could end Team Rocket forever. One victory and no one would be harassed, bullied, or robbed by the notorious gang ever again. A competitive gleam shined through Red's eyes as he stared his opponent down. Red's hands went to his Poké Balls as he removed them and threw them all to the floor before taking several paces back, "I'll take your bet, but this is going to be a fair fight."

"Yes," a fire seemed to light in Giovanni's spirit, "that's what I love about you!"

The two stooped into a position ready for the mad dash for a Poké Ball. The tension made the room seem silent. The stares continued as each awaited the perfect moment for their death duel to begin. A sliver of ice forming in the mist fell to the floor and with but the faintest ping the two were off. Red reached his Poké Balls and immediately grabbed the one he knew contained… "SNORLAX, MEGA PUNCH!" The giant Pokémon materialized from its ball, its great paw already reeled back and glowing before driving forward into another Pokémon fresh on the field. Red's eyes widened as Giovanni's Nidoking actually caught the punch and dissipated the energy behind it.

"Sometime's it's best to use your opponent's speed and anxiousness against them, you'll learn that soon. Nidoking! Seismic Toss!" Giovanni commanded and his Nidoking actually lifted the huge Snorlax into the air.

"No way!" Red shouted in awe and panic as his Snorlax was slammed hard onto the floor. The foundation of the decrepit Viridian Gym crumbled under the impact of the incredible slam. The whole building shook violently as cracks formed along the floor and spread up the pillars supporting the ceiling. Snorlax began to stand but its lumbering movements caused even more vibrations to the structure and parts of the ceiling were beginning to fall. "Snorlax return!" The massive dozer was recalled to its Poké Ball just as a wooden beam fell over the spot he had been standing.

Red scrambled to collect his other Poké Balls but as the floor collapsed further they began to roll away in random directions and under debris. He managed to grab only a few when another large ceiling beam began to fall. He turned to see it falling toward his still unconscious Poliwrath. Without a moment of hesitation Red dashed for his oldest Pokémon, "Poli, no!" He leapt through the air and shielded Poli with his own body not even a second before a large wooden beam fell upon them. Red howled in pain as he was pinned by the beam that had fallen on his back. He managed to push himself up enough to roll the beam back but the weight on his legs caused him to have to twist in abnormal ways in order to free himself.

Once free Red managed to find Poli's Poké Ball and return him to safety. He then limped as fast as he could from the collapsing building knowing the Poké Balls were sturdy enough to keep his other Pokémon safe for the time being.

Red barely made it through the door when a thunderous roar signified the entire building had caved in on itself and huge clouds of dust rose into the air. Red tried to take a few breaths to compose himself, but he realized in the midst of the confusion that he had completely lost track of Giovanni. He squinted his eyes willing them to see through the dust to find the first trace of his opponent. An eerie laugh echoing through the rubble told him he had been spotted first.

Red braced himself as several sets of monstrous footsteps approached him. The intimidating figures of Nidoking, Nidoqueen, Rhydon, and Dugtrio all emerged from the dust cloud together, "It would seem in the time it took you to safely whisk away a few of your Pokémon I was able to pull out more of mine. Say hello to my A-Team!"

Red grit his teeth and threw the first Poké Ball into the fray, "SAUR!" In a flash of light the great plant beast Venusaur stood formidably before Giovanni's four ground Pokémon.

Not entirely surprised by Red's team, Giovanni pointed forward, "Rhydon, use Horn Drill!" Energy swirled around Rhydon's horn as it dashed forward and ready to impale the Venusaur.

"Vine whip now!" Saur's vines emerged and wrapped around the giant rhino tightly and were strong enough to lift the creature from the ground, spin it in the air, and throw it back toward the nido couple.

"Not bad," Giovanni smirked. Red wasn't sure what Giovanni had up his sleeve next, but no other orders were being given. It was then that Red realized Dugtrio was nowhere in sight.

"Watch out from below…!" Red hardly finished his warning before the ground began to shake and with a great rumble a fissure split open, one wide enough for the Venusaur to fall into. Surrounded by high walls, Saur was effectively immobilized, "No…"

The other three ground types were back on their feet and surrounded Saur quickly. Red needed time, and something that could catch Giovanni off guard. As he was beginning to understand his opponent, Red looked up at the sky towards the sun.

Giovanni's eyes widened as he caught Red's skywards glance. He realized if the Venusaur managed to absorb enough energy to use Solar Beam things could turn disadvantageous for him. "Quake!" he commanded his Pokémon as they all immediately focused on quaking the ground hurling huge amounts of rock and dust into the air. Red tried not to smirk as everything around them began to darken once again.

Having thwarted Red's strategy, Giovanni crossed his arms and waited a moment before sending his Pokémon in to finish the job. He squinted his eyes as he noticed a faint glimmer through the thick dust. A low grumble echoed through the area and immediately Giovanni knew it was no Venusaur making that noise.

Red waited as the dust cleared just enough to have a straight shot, "HYPER BEAM!" The dust cloud was split asunder as a beam of energy cut through it and impacted Giovanni's Nidoking dead on. The huge Pokémon was thrown back into the rubble of the gym where it flinched and then fainted. No longer hidden behind the dirt was a mighty Gyarados who let out a leviathan like howl which immediately intimidated all of Giovani's Pokémon.

Giovanni cursed under his breath. Red had played him well to have delayed him long enough to pull out another Pokémon, especially one as formidable as a Gyarados. Giovanni threw another Poké Ball into the fray and a Rhyhorn materialized from within it. With a stomp of his foot Giovanni regained his Pokémon's attention, and with a wave of his hand he sent them charging the sea serpent. He had to take it down before it recovered from firing the hyper beam.

It would be a gamble to put the next phase of his plan into action, but Red knew he was looking at his best opportunity. The path was clear now that Giovanni's Pokémon had moved so Red held a Poké Ball out. The beam collided with the Venusaur and returned him to the ball for just as long as it took for Red to flip the ball and release Venusaur again at a more favorable position. "Now, Razor Leaf!"

Though disoriented from the maneuver, Saur shot volleys of leaves at Giovanni's approaching Pokémon. Not much of the attack hit, but they did stop which bought Gyara a little more time.

Before the attacking Pokémon carried forward, Giovanni stomped his foot on the ground. A slight rumble was felt just before the Dugtrio burst upward from underneath Saur and hurdled the leafy beast meters into the air. Red's eyes widened in panic but he couldn't afford to lose his cool now. Saur had bought them the time they needed, "Hydro Pump!"

Gyara roared again before releasing a torrent of water from its mouth. The water impacted the fresh Rhyhorn who took the full brunt of the attack and was knocked out in a single blow. That cold chill ran down Red's spine again and by reflex he threw his Snorlax back into battle. "LAX! DEFENSE CURL!" Lax appeared back to back with the Gyarados in a defensive position just in time to shield it from a surprise Ice Beam launched by Giovanni's Cloyster which had been lurking in the back.

"Absolutely amazing, to think your intuition as a battler would be this refined." Giovanni praised Red's work. "You fight very well, and are proving to be a far greater challenge than even I was expecting. No one has ever done this to me before…"

Though Giovanni was talking Red continued to focus on the field. He was doing well but was still surrounded and couldn't afford to let up yet. He knew if he could hold on like this for a bit longer that he could turn this around and take control of the battle. Though he was hardly conscious of it, Red had several scenarios playing through his head and was calculating the outcomes of each one.

Giovanni could tell Red was only a move away from turning the tide on him. He couldn't allow this, "Though you've done well, this is a battle I can't afford to lose!" Giovanni snapped his finger, "You and your Pokémon are fast on your feet, but again sometimes you have to use your opponent's speed against him, Trick Room!" The Cloyster immediately gave off a brilliant light. Red turned to look at it but the rest of the world darkened around him as he watched himself and his Pokémon moving in slow motion as everything else roared past him faster than his eyes could keep up with.

The effect faded and Red immediately noticed the cloyster had moved around Snorlax's defense.

"Cloyster, use Ice Beam! Rhydon, Nidoqueen, Take Down!" Without a chance to react, Gyara took the full brunt of each attack and howled in pain as ice encased it to keep it still while the Rhydon and Nidoqueen charged at it from opposing sides. Their attacks sandwiched the sea serpent and shattered the ice sending frozen scales flying off into the distance. Gyara's great struggling howl continued to wail loudly in the distance as the beast collapsed to the ground.

"I've never seen a move like that before…" Red whispered to himself out of shock. He gritted his teeth and tried to keep his determination high, "We're not done yet!" Red turned his hat backwards, "Mega Punch!"

The hefty Snorlax lumbered forward and threw its fist at the Rhydon. Rhydon flew back several meters but remained standing. It was obviously hurting from both the recent Take Down's recoil as the strong punch.

"You are incredible Red, so passionate even in the worst of situations." Giovanni seemed to pause the battle with his words, "I truly am tempted to allow you to go on living this way, full of life and energy. I don't want that to end…" The man's gaze darkened as he looked away, as if unable to meet Red's questioning eyes, "but if I'm going to succeed then I need you with me and there is far too much at stake for me to turn back now."

"I don't understand…" Red was unsure what points Giovanni was trying to make. It all sounded like gibberish to him, "What do you mean by all that?"

"No need to concern yourself with that yet," Giovanni turned back to the battle. "What you should be more worried about is the ground of which your Snorlax relies HEAVILY on!"

The quaking ground signified Dugtrio bursting through the ground once again, this time with Snorlax as its target.

Red grabbed the brim of his hat and turned it back around as some kind of signal, "Solarbeam!"

Giovanni's eyes widened as he turned to the Venusaur who was indeed back on its feet. A powerful blast erupted from its flowering top. Dugtrio's head burst from the ground within range of Snorlax but the Solarbeam made impact first and flooded the area with a crashing light.

"That's…" Giovanni shielded his eyes from the light to try and see what was going on and just barely caught the shadow of Snorlax as it emerged from the light and Body Slammed his Nidoqueen. The Nidoqueen was bounced from Lax's belly and skipped across the ground like a stone over water until she crashed into more of the building's rubble. The titanic nido still managed to slowly climb to her feet, but it was obvious she was hurting bad.

Giovanni looked around at his team, Dugtrio was out like Nidoking and Rhyhorn, Nidoqueen didn't have much fight left in her, and his Rhydon was also wearing down. On the other side of the field Red's Venusaur could barely stand, but the Snorlax still had fight left in it. The ludicrousness of Red's ability was finally setting in, "He's doing it…" Giovanni said to himself in barely a whisper, "with but three of his Pokémon he's still doing it… The blood of a champion…" Giovanni shook his head vigorously to recompose himself, "You still won't win! Rhydon, use Fissure on that Snorlax!" Rhydon seemed to grow in size and focused all its strength into one spot in its fist.

Red had heard of Fissure, a move that guaranteed defeat of a Pokémon if it hit, "Get out of the way Lax!" The lumbering Snorlax was too slow this time and Rhydon's power collided with its oversized body. Lax's eyes actually opened wide as it was ripped through several meters of solid rock as the attack split the earth apart through sheer force. Lax continued to quiver until the Rhydon pulled back its fist and allowed heavyweight to crumble to the ground.

"Lax, no…" Red stared in disbelief as the Rhydon and Nidoqueen regrouped and converged on his weak Venusaur. Venusaur swatted at them with vine whips, but in its current state Rhydon was easily able to knock them away. "No…" Red stumbled back and fell to his knees, "I…" He had given the battle everything he could, but the shock of what that meant was still setting in as he willed himself not to shed any tears, "I…"

Giovanni's expression showed he was taking no pleasure in this as he slowly approached the boy and solemnly asked, "Are you giving up?"

Red held out his Poké Balls and recalled his defeated team. Silence reigned over the area for a long moment and then Red finally nodded.

"You love your Pokémon a great deal don't you?" Red answered again with only a nod. "It pains you to see them suffer, you'd much rather put yourself in danger than see them hurt." Giovanni had taken notice of Red limping earlier and upon closer inspection could see the boy's clothes were torn and a few bloody smears were visible through his shirt and pants. "Please join me and we can save all Pokémon from a far worse fate that still looms over us all."

Red's mouth hung open for a moment as he looked up to Giovanni as if not quite comprehending the words he was being told, "But Team Rocket does horrible things to Pokémon. You steal, hurt, experiment, and do all those horrible things to Pokémon and people just for fun without a care about it. How is that saving them?"

A hand calmly lowered onto Red's shoulder, "You don't yet understand the purpose of Team Rocket and our experiments. Nor do you understand the evils of the world and what must be done to stop it. I assure you Team Rocket does no more than what is necessary to see to the continued prosperity of Pokémon everywhere."

Red turned and tried to push himself away, "N… No! I don't believe you! I won't be part of that!"

The look in Giovanni's eyes darkened, "But we had a deal."

All of the times Red fought against Team Rocket flashed through his mind. They weren't nice people, and he didn't want to be like that, "No… I… I can't!"

"As I said," Giovanni gripped on tighter to Red's arm, "you don't yet understand… but don't worry… you soon will."

True fear flashed briefly in Red's eyes as he knew not what would happen next. But in the next moment he felt a prick and those same eyes dulled. He finally broke away from Giovanni's stare and looked down to his arm which the man held tightly and saw the syringe Giovanni had just injected him with.

"You can't… can't…" Red's eyes closed and he fell limply forward, supported only by the grip Giovanni still held on him.

The last words Red heard before his consciousness left him entirely were, "You will soon understand… all of this was for you…"

* * *

 **End Chapter**

This chapter of course ended up being not too different from the original. I feel this accomplished the goal of setting a quality and detail standard at a higher level though as well throwing in a few more elements of foreshadowing that should remain consistent as the story progresses now.

Thanks for reading and we'll see you next week!


	2. Maroon Resistance

Notes:

I shouldn't be editing while drunk, but meh…

There were a lot of scenes in the original version of Rapture that were implied and hinted at but never witnessed by the reader so to say. I'm really hoping to flesh more of these scenes out and give everyone a better idea of everything Red has gone through during his "captivity".

Big thank yous go out today to:

Phz – Hopefully word starts getting out that this is being completely redone… Maybe I should have created an entirely new story entry, but I figured this would get word out better to all of the previous readers, as well as keep spoilers away from new readers.

Bertrand Benach-Tarski – I'm really excited about this too! I want to see this story completed so bad! I have so many other story ideas in my head, but I forced myself to put everything on hold until this one is done.

The Wandering Cat – I don't know what to say. I am ecstatic as well as terrified to find someone encouraging along this path of grunge like torture that I subject my childhood memories to. Don't get me wrong, I absolutely love it, and thank you so much for helping with that push for detail despite how gritty and depraved it may become. This chapter already has a lot to thank for your comments. I definitely hope to get more reviews like that!

There's a lot of ground to cover, so thanks for coming back to another chapter of Rapture, and I hope you enjoy!

* * *

 **Chapter 2: Maroon Resistance**

* * *

Sometimes consciousness plays tricks on people. As it returns it can be difficult to tell whether a room is white or if there is an incredible amount of light flooding it. Red tried to clear his head enough to tell the difference. Everything was silent though, he couldn't even hear his own breathing.

From within the unidentifiable white there were clacking steps almost like hooves but not quite like anything Red had ever heard. Then before him Red saw the figure of a creature he'd never before witnessed. It towered like a giant walking on four legs but with many arms. It was almost impossible to describe even though the creature was standing directly before him. It was like it existed in a state of flux with parts of its own body that may or may not have actually existed at all. Red wasn't sure if this was some kind of unknown Pokémon… or something else entirely.

The two stared at each other, but Red found himself unable to trace any kind of recognizable emotion from the mask like face. Then, in even greater mystery than it had arrived in, the creature simple faded back into the white.

Red blinked away the haze from his eyes as he realized he was lying down. He looked around and saw he was in what looked like some kind of hospital room. His body felt sore and he noticed his torso was wrapped in several layers of bandages as well as his left leg. He tried to sit up but found his arms and legs wouldn't move much. It finally registered that he was strapped down to the bed.

It took a moment for the memories to come rushing back into Red's mind. There was a battle he fought against Giovanni and… he had lost. And they had made that bet. Panic suddenly set in and Red started struggling against the binds, he needed only a bit of play to free his slender arms.

"Ah, you're awake," Red stopped for a moment and looked to the doorway to see Giovanni now standing there. He glared angrily at the man who stepped closer to the bed. It was hard to read Giovanni's face, his expression was somewhere between pity and resignation, "Perhaps you'd feel better knowing all of your Pokémon are safe."

"What about the ones that were buried under the gym?!" Giovanni silenced Red as he pulled out a familiar Poké Ball belt and set it on the bed next to is owner. All six Poké Balls were safely attached to the belt. Red noticed Giovanni's hands were dirty and scuffed as if he'd been laboring at something. The room fell silent as Red looked over all his Poké Balls, "How long have I been asleep?"

"Only a day," the answer was spoken plainly.

Another silent moment passed, "Why…" Red shook his head as he tried to comprehend what was going on, "Why didn't you just abandon them, like you would have any other Pokémon?"

Giovanni shook his head, "You have the wrong idea about us Red. Would it surprise you to know I find anyone who would do something like abandon their Pokémon to be a disgusting excuse of a human being? I would punish them severely myself if given the chance."

"But all the Pokémon you steal and hurt…" Somewhere inside Red wanted to believe that even Team Rocket wasn't just inherently evil, but he'd seen them do so much and had formed his opinions quite solidly already.

"Sometimes Red… sometimes the best methods don't lead to the best results. Sometimes you have to do something bad so that something good can survive. This is sadly a fundamental truth to the world." Giovanni pulled one of his own Poké Balls from his coat and seemed to examine it, "I don't want to hurt anything. Sometimes though if small sacrifices aren't made then far worse things could rain down and ruin everything."

Red was having difficulty piecing together the cryptic words, "I don't… understand… I don't believe you."

"You're young, naïve… innocent. I was like you once. I believed that courage and a strong heart could accomplish anything. And then I discovered just how wrong I was," slight emotion started building in Giovanni's voice, "You haven't seen what I've seen so you don't know what's out there." The man kneeled down to look into Red's face at eye level, "Now I will do what must be done not to destroy, but to save the world Red. Many wouldn't agree with my methods but if there's a chance to make a difference then we must not hesitate and take that chance like our lives depended on it."

"I don't… know…" Red had never felt this kind of pressure being placed on him just from someone's words before, "I can't… there have to be other ways to do whatever you're doing without hurting others."

"We've tried, and there isn't any other way," Giovanni responded instantly.

Red snapped back, "Then I won't help!"

Giovanni stood; an angered look crossed his face, "Don't be so quick to decide… First there are things you must see, then we will speak again." Giovanni picked up a remote control and turned a TV on as a video began to play. He took Red's Poké Ball belt and then quietly left the room.

Once Giovanni was gone Red returned to pulling on his restraints but they wouldn't budge. Red hadn't paid attention to the screen at all and when he finally looked after giving up out of frustration to free himself his lips began to quiver. On the screen were some of the most horrific scenes and images he had ever seen in his young life. Violence… bloodshed… destruction…

The videos continued to play all night long. Red kept looking away, he closed his eyes, played songs in his head, anything to block the sights and sounds from the TV on the wall. He thought through old rhymes and lines from old school text books, anything that might keep him from acknowledging the existence of the entire wall in front of him. Even sleep came difficult as the videos played on.

Sometime in the morning the screen had gone blank. Red hadn't even realized there was nothing on the TV until the door opened and Giovanni returned. Red looked up at the man not quite feeling well to his stomach, "Why would you show me something like that?"

Giovanni took a deep breath before beginning, "Because that's the world you don't know yet and whether we like it or not it's a truth we have to deal with."

"No…" Red shook his head, "You're lying to me, none of that was true…" He shut his eyes and looked away from Giovanni, "NONE OF THAT WAS TRUE!"

"How I wish time was a luxury we could afford…" Giovanni sat down by Red's bed, "How I wish this could have waited until you were a bit older and ready." Giovanni chuckled ironically to himself, "Though I can't say anyone would ever truly be ready for something like this. It isn't fair to you; I admit that whole heartedly."

The two sat through another extended silence. Red refused to open his eyes and acknowledge Giovanni's presence while Giovanni appeared to be lost in thought.

"This isn't going to get us anywhere…" Giovanni stood from the chair, "Would you like to see your Pokémon?"

Red finally turned to the man, "Yes…"

"Then promise me you won't do anything stupid and I'll take you to them," Red nodded solemnly.

Giovanni reached down and undid the buckles holding Red to the bed. The first thing Red did was stretch as hadn't be able to move more than a few inches for over a day, "Thank you."

"Follow me," Giovanni ordered as he guided Red from the room down a few halls. There weren't any windows so Red couldn't tell exactly where he was, but the compound was huge. There were a lot of people in Team Rocket uniforms bustling about who seemed to just ignore him as he was led through the hall by the Rocket Boss. They reached a door that read "Habitat Zone F" and Giovanni swiped a card through a slot nearby to open it.

The two stepped out onto an observation deck of sorts. They were surrounded on all sides by thick windows which overlooked a luscious forest replica, "It looks like…"

"The Viridian Forest, I know…" Giovanni pointed to a spot between a few trees, "See there?"

Red followed the direction and saw Saur resting over the corner. Once he caught sight of his Venusaur his Aerodactyl flew by the glass, his Poliwrath and Gyarados were swimming in a pond, and then a Pikachu poked its head out of the bushes.

"Pika!" Red shouted hoping to get the rodent's attention. Pika didn't seem to hear him though and continued collecting berries and nuts.

"The glass is mirrored and soundproof. It's meant to allow observers to watch their Pokémon in a more natural state, to see how they act without their trainer looming over their every move." Giovanni leaned against the bar and joined Red in just enjoying watching the Pokémon be themselves.

Tension visibly left Red as he saw all of his Pokémon were healthy and together, "This is a really nice place you have for Pokémon."

"We have 8 rooms like this, each suited to different Pokémon types," Giovanni explained.

Even Professor Oak didn't have that many different environments in his lab for the Pokémon he cared for, "That's a lot of work to set up…"

Without much thought to his words, Giovanni responded with, "It's worth it to keep the Pokémon motivated."

"Motivated…" Red repeated absently. There was something cold and impersonal about that word to Red.

Giovanni sighed, "That should be enough time, there is more you must see."

Red's lips parted into a frown as he pushed away from the window and followed Giovanni from the room. On the other side of the glass, Pika's ear perked up and he looked to the mirrored wall as a sudden sense of gloom overcame him. In the reflection the clever Pikachu caught sight of an air vent.

Red followed Giovanni back through the building. Though most of the surrounding members of Team Rocket did little more than glance their way as he was led through the offices, one man in a coat called over to Giovanni and jogged across the room to catch up.

"I explicitly said I was not to be bothered by matters this morning," Giovanni grumbled out of annoyance.

"I apologize sir," The man bowed apologetically but held out some documents, "but this is extremely important. The Johto lab is at a halt until we can have you authorize expenditures."

Giovanni kept an eye on Red as he glanced over the documents. Red leaned back against a desk while Giovanni took care of the unexpected business.

"They want what?" Giovanni quirked an eyebrow at the request, "Never mind, I'll talk to them myself…" He then motioned over to one of the familiar henchmen, "Ken, I need you to take our guest back to his room, and run series B."

"Alright sir," Ken looked over Red, "Does the kid need to be tied down?"

Giovanni made eye contact with Red in an appraising fashion, "I don't think that will be necessary, just lock the door."

"Sounds good, let's go squirt," Ken prodded Red forward and pushed him back into the hospital like room. "The boss said series B right?"

Red sat down on the bed and looked up pensively at Ken, "Have you seen these videos?"

Ken looked up for a minute and frowned at Red before he turned back to the console so Red couldn't see his face, "I seen it all once."

"How did you…" Red gulped as he tried to keep his stomach in check from the mere thought of those videos, "…stand it?

"It's scary stuff huh?" Ken nodded though he still didn't turn around, "I s'pose it was better than the alternative."

The thought of a worse alternative confused Red, "And what was that?"

"Livin my whole life in the dark, not knowing…" It didn't make much sense to Red how not knowing something so sickening could be worse than having to deal with it.

Ken didn't turn to look at Red again as the video started up. The young man pulled a card from around his neck and swiped it through a slider on the door to lock it as he left.

Red waited a few minutes and tried not to pay attention to the video at all. He reached into his back pocket and pulled a security card like Ken's that he'd managed to slip off the desk in the office room. He padded to the door quietly and pressed his ear against it to make sure there was no one just on the other side. Once confident he quickly swiped his stolen card on the door slot. The small light gave off a green glow and then the door unlocked.

As quietly as he could, Red pulled the door open just a crack to see who might be nearby. The closest person was a ways off and they seemed to be distracted by something in a different direction. Red slipped out of the room and gently shut the door behind him.

Remembering the way to the Pokémon observatory, Red snuck under desks and cubicles to avoid detection as he worked his way back to his team. The offices were laid out in a cubicle maze that made progress much more difficult that the straight hallways. Red held still and breathed quietly as he hid under a cabinet and looked from side to side for his next nearby hiding spot. He was about to make a move when two sets of rocket boots stepped out in front of him, "Have you heard the news from Sinnoh?"

Red pushed himself as far back as he could to try and stay hidden, "No, what's going on over there?"

The next desk was about ten feet of open area away, Red knew there was no way to get there with guards standing nearby, "Apparently, Team Galactic caught one of the phantoms."

"Wow," The other grunt shut the cabinet with a bit of a slam causing it to vibrate loudly over Red's head, "I wonder if that's good news or bad news for us."

The two started walking away, "I don't know, but it seems the boss is ordering a fallback to Johto, he wants everyone on the street beats in plain clothes from now on."

Red waited a moment for things to clear and then made his move through the office again. Eventually he caught sight of the door to the habitat but it was in a large open hall with no cover. Several more people were walking nearby so Red patiently waited for things to clear.

The last person Red was watching turned down the next hall so he finally dashed for the door. He had the stolen card out and swiped it through the reader. Unlike the previous door which simply unlocked for him, the card reader on this door made a dull buzzing sound and blinked with a red light. He tried swiping the card again but got the same reaction from the device.

"The boss locked it so only a general's card can open that door right now," startled Red turned around and saw the human behemoth Lieutenant Surge watching him, "A card like mine see?" Surge twirled the card on his chain, "So what's it going to be, little mouse? You want the card from the big bad cat?"

Red's fist clenched as he watched the man step closer. Before Surge got too close, and without any warning, Red turned and dashed down the hall, "Yes! Now the fun starts!" Surge immediately gave chase, his thunderous footsteps clunked far more sinisterly than the pattering of Red's bare feet.

Most members of Team Rocket were caught off guard as they saw Surge giving chase to the boy through the office. They watched almost stupefied rather than aiding their general. Not being aware of the building's layout, Red was taking turns randomly, and trying not to get too close to anyone who would try to catch him. Surge on the other hand was shoving people and objects out of his way, his singular objective to run Red down.

Finally Red's lack of knowledge of the building became his downfall as he turned down a hall which led only to maintenance supplies, "It was fun while it lasted at least." Surge approached from behind, his colossal build took up most of the hallway.

Red shut his eyes and waited as Surge stepped closer. "Ki!" A familiar squeak sound and the cackle of electricity sounded off behind Red who had enough sense to duck out of the way as a Thunderbolt shot through the duct work and knocked Surge back to the other side of the hall.

"Pika!" Red shouted excitedly as he pulled the grating off the small exhaust vent and allowed the electric mouse to hop into his arms. "Come on, we have to get the others!" Surge was still groaning as Red leaned over him, plucked off his security card, and ran back down the hall.

Now with a Pokémon at the boy's side and no sign of Surge, some of the Rocket Grunts started panicking, "GET HIM!"

"Thundershock!" Red commanded as his faithful Pikachu hopped into the air and unleashed volleys of electricity at anyone who dared approach them.

"I've got him!" A grunt yelled as he threw a Poké Ball in front of Red and released a Magmar. Smoke was released with the molten Pokémon's breath as it towered over the approaching duo, "There's no way he can beat a Magmar with just a little Pikachu!"

"There, Pika, Thundershock!" Pika followed Red's motion precisely and shocked a nearby fire extinguisher. The shock weakened the casing enough for the pressure inside to blow its contents out and doused Magmar with the extinguishing foam and filled the room with a smoldering fog. "Now Thunderbolt!" The weakened Magmar was unable to endure the electric blast and it fell as Red and Pika continued their dash while hardly slowing their pace.

"I think we're almost there," Red spoke encouragingly to Pika as they jumped over desks, dove under tables, and knocked over cabinets to slow their pursuers. They had put some distance between themselves and most of the Rocket grunts when they rounded another corner and slid to a stop.

Ken, Al, and Harry, the three members of Team Rocket known as the Elite Trio blocked Red's path with their Pokémon Tauros, Slowbro, and Muk out as a formidable barrier. The three stood dauntingly behind their Pokémon, "Sorry kid," Ken started, "But orders are orders, and no one gets past the Elite Trio when we're together!"

Red knew he couldn't afford to give up momentum now. He assessed the area as he pleaded with the Trio, "Please you guys, you need to let me go, this isn't right and you know it!" Underneath Red's feet was a thin carpet, hopefully enough to provide some insulation.

Al crossed his arms and looked down at the boy, "Maybe you'd see what's right if you'd stop fighting every step of the way."

The fluorescent lights in this room hung low from fixtures wired to the ceiling.

"We don't want to hurt you but we will if that's what it takes to reel you in and get you to settle down then we're not afraid to do it," Harry stood with his hands at his hips joining the others in an authoritative pose.

There were still no windows around; all the light in the room was artificial. Red memorized as much of the room as he could before pointing to the wall near him and shouting, "Thunder!" The energy which had built up in Pika's cheek pouches as it ran gave off a menacing glow before it released all at once and entered into an electrical socket at Red's side. The lights in the entire area gave off a brighter glow for a moment before they all exploded in a glass shattering shock, and then everything went dark.

"I can't see anything!" Al yelled.

"Quiet! Don't let him sneak by!" Harry ordered.

Red took a few steps back and sank under a table while remaining mostly still and quiet. Pika stood at his side mimicking the silent demeanor.

"He's gotta still be here, can you see anything?" Ken rubbed his eyes trying to become accustom them to the darkness.

Rocket grunts were stumbling around in the dark, hoping to find some kind of auxiliary light source. Several minutes went by and Red noticed everyone around him was starting to stumble less.

"I can make out…" Al began as he peered into the dark, "Wait… HE'S UNDER THE…"

Red hid his face in his hands, "Flash!"

Pika gave off an astonishing ray of light which doused the eyes which had adjusted to the darkness in an unforgiving bath of luminescence.

"AHHHH!" Everyone in the room began to scream, the sudden light was literally painful. Pika kept the flash as bright as he could for several more seconds and then all returned to darkness. Most of the effected Rocket grunts fell to the ground and continued yelling into their hands.

Red jumped up, grabbed his Pikachu, and resumed the dash for the habitat where the rest of Pokémon were still held.

"That's the door over there!" Red shouted excitedly as he pulled Surge's card out to open the door. A buzzing sound registered in Red's mind and as he turned to look he saw a large Beedrill flying towards him at top speed. Red tried to duck out of the way but this Beedrill was faster than most and maneuvered itself to bite down onto the card Red held in his hand. Red wasn't about to let go of the card, and Pika was approaching to assist his trainer. The Beedrill swiped at Red with its stinger forcing the boy to duck in order to rip the card from his hand. It then swiftly dodged away from the Pikachu and flew back down to the other end of the hall.

"You've caused quite enough commotion for one day," The Beedrill set the card back in Giovanni's waiting hand.

"Give that back!" Red shouted as Pika charged down the hallways and leapt for the Beedrill, thunderous sparks forming around his body. A large fist slammed down from behind the corner over Pika's head and knocked the rodent to the floor. Giovanni's Rhydon emerged and stood in a defensive position in front of its master.

Red's eyes looked from object to object around the room, looking for something, anything he could use.

"Still he seeks to gain the advantage in battle," The clacking of hard heeled footsteps approached from behind Red as turned to see Sabrina approaching, an Abra in her arms.

Giovanni nodded, "Do it."

The Abra in Sabrina's arms opened its glowing eyes and stared directly into Red's. The boy grit his teeth as he resisted the psychic Pokémon's power. Pika noticed the problem and hissed as viciously as he could as he jumped back to his feet and ran back to his trainer's side. He stood guard with his tail up in a threatening manner.

Red's head throbbed in pain but he refused to go down. Giovanni snapped his finger and again the Rhydon charged. Its Horn Drill pointed down at the small electric type. Ready for the move, Pika jumped out of the way, turned, and ran up the massive Pokémon's back, "Tail whip!" Pika was small but he was able to use the giant's momentum against him as he landed the tail whip to the back of great ground type's head. The lumbering Rhydon lost its balance and fell forward.

Abra had yet to lift off its psychic attack on Red's mind. Red held his hands to his ears and willed his own brain to not give in or shut down. He groaned in strain as he pointed to the Rhydon again, "Take Down!"

Pika jumped off the Rhydon and with uncanny momentum latched onto the ceiling above him for a moment before forcing himself back down with a bound strong enough to shatter the ceiling tiles behind him. Pika hit the Rhydon's back causing the titan to spread on the ground and howl in pain.

"Even his Pikachu is far from ordinary…" Giovanni couldn't help but admire as he gauged his next move.

The Abra in Sabrina's arms focused harder, intensifying its psychic assault. Red gripped his head harder and screamed as his nose began to bleed and blood vessels in his eyes broke open.

Though Rhydon wasn't out, Pika turned his attention to the Abra attacking his trainer. A terrifying electric current built up around the small rodent causing the lights in the room to fluctuate before the attack was even launched. The voltage formed some kind of field around the Pikachu as it charged toward Sabrina and her Abra in a vicious tackle.

"Beedril, Agility, go!" Giovanni's Beedrill moved to intercept the Pikachu. It barely managed to place itself between Pika and Sabrina in time and took the full brunt of Pika's attack. The hallway lit up in a magnificent light and expelled the Beedrill from its walls like a cannon.

Both Giovanni and Sabrina looked on with widened eyes, astonished by this Pikachu's display of power. The move took its toll on Pika as well as he struggled to remain standing.

Seeing an opportunity, Giovanni snapped his fingers. The Rhydon picked itself up from the ground and ran forward. With enough momentum behind it, Rhydon head-butted the Pikachu into the wall, leaving a small crack along the plaster surface. Pika fell from the indenture its body left, unconscious by the time he hit the floor.

"NOO!" Red continued to struggle and took several labored steps through Abra's psychic attack toward his Pikachu.

Sabrina placed her hand on her Abra's head to amplify her thoughts through its powers. Red's mind was invaded with notions that he should stop, that team rocket wasn't his enemy, that people he'd known all his life had lied to him, that he should shut his eyes and sleep.

Red made it to his Pikachu. He kneeled down beside it only moments before he finally collapsed from mental exertion. The psychic attack ended and Sabrina immediately fell to her knees as well. Out of breath, she looked as though she'd run a marathon.

A sigh of relief escaped Giovanni as he recalled his Rhydon and Beedrill and stepped closer to the group. "Are you alright?" He asked Sabrina first.

She nodded, "I rarely have to exert that much power on an individual…"

"I see…" Giovanni helped Sabrina to her feet and returned to Red's side. He caught sight of the rectangular shape in the boy's pocket and pulled out the stolen security card. "If given even the slightest chance, he will take it…"

Koga approached from behind Giovanni, "And make a right mess of things while he's at it. We should just be rid of him."

Giovanni looked around the office space. Electrical burns marred the walls, papers on desks were burning, an entire wing was pitch-black with shouts emanating from within, and people were still evacuating the sauna like room where a Magmar was smoldering. He knew Surge was probably lost in the midst of all that as well, "Koga, return Surge's security card to him, and see he assists in cleaning up this mess."

"And the boy?" Koga was obviously not at all enthused by how things were turning out.

"He will be punished. He will know these sort of antics will not be tolerated," Koga scowled but still bowed and took the security card back with him.

Orders given, Giovanni stood over Red in deep contemplation, "How _did_ he acquire one of his Pokémon…?" Giovanni asked himself as he entered the habitat where Red's Pokémon were being kept. He spent a moment observing the remainder of Red's Pokémon who were still in place where they were supposed to be. A glimmer on the ground caught his attention, "Metal?" He squinted his eyes to see better and made out a metal grating that had pieces of vines still attached to it. He looked up and could obviously see the open vent where it had come from. And just below the tiny crawl space were large heavy footprints, a Snorlax's footprints. "So even without their master they will still work together. You've trained them well…"

Giovanni turned and marched from the observatory; his face an emotionless mask.

Sabrina returned to his side, "How would you like to proceed?"

Giovanni came to an unexpected stop; however Sabrina remained in perfect sync with Giovanni's steps. The man looked to her with a grim expression on his face, "Know I take no pleasure in doing what must be done."

"I understand," Sabrina stated enigmatically.

"Of course you do…" Giovanni sighed, "I will need assistance from all of you. As much as it pains me to say this, if we are to count that boy among our numbers then first he must be broken."

Silence imbued the space between them for several tense moments. Sabrina finally nodded and the two continued on to make their preparations.

* * *

 **End Chapter**

Never underestimate a boy and his Pikachu. I'm hopeful this chapter gives a better impression of how much Red is struggling not just fall into a new or different life.

Terrible things are yet to come. Thanks for reading, please leave a comment and we'll see you next time!


	3. Umber Foundations

Notes:

This chapter actually pained me to write. I feel the need to state again that this is a work of fiction and that I do not condone any sort of the actions that take place in this chapter.

I'm positive I'm going to have a few more mistakes than normal in this chapter. It's kept me up way past the time I should be going to bed for class and work tomorrow, but I should be able to survive as a zombie and do some editing later.

And thank you much for the reviews from the last chapter!

BlueMoonLove1999: There has to be hope in order for there to be real tragedy. But there has to be tragedy in order for there to be greater triumph. Thanks a lot for coming back to the story and reviewing again! It's so cool to see someone from the original still interested.

The Wandering Cat: Your reviews are amazing! Thank you! You're definitely giving me awesome ideas to help tie in everything together and keep the detail to a level where it needs to be. I've definitely got plans to include several more characters that never made it to version 1 of this story. I've also got a fairly good idea how to handle the upcoming concerns soon.

Zarclonia: Again, it's so awesome to see people come back to read the story after reading the original. I hope this doesn't disappoint. I'm definitely trying to include some more foreshadowing of certain details from early on this time. Hopefully we'll have some awesome moments when they all tie in together.

Guest: Thanks for the comment as well! I hope you enjoy!

* * *

 **Chapter 3: Umber Foundations**

* * *

Hours passed before Red finally stirred. His vision was blurred and his mind was still jumbled as he awoke. Finally he realized he wasn't lying down, but was hanging vertically on a cold metal surface. He tried to move but found he was strapped to whatever he was on tightly. The room was dark and it was hard to make out detail except a large screen in front of him, a metal door to one side, and a mirrored wall to the other. He noticed his jeans had been removed, his underwear now the only shield to his dignity.

Red pulled on his binds, despite the sensation that they were cold, steel, and unforgiving. They dug into his skin with no sign of any give at all.

After some time there was a loud beep and the door opened allowing Giovanni to enter, "I'm disappointed in you."

Red barked back "You think that's the most I could…"

"Once again you miss the point…" Giovanni sighed loudly as he appraised the boy strapped to the metal apparatus, "I know very well with enough time you could tear this whole place down and hardly anyone could stop you. I had hoped though that you were beginning to understand why…" Giovanni interrupted himself as he tried to piece together his words, "You see, in order to understand you would have to change… and you haven't changed at all in… how long has it been since we were looking for Pokémon fossils together?" Giovanni paused for a moment, his gaze downcast, "It has been a long time, and time is running out. So I'm sorry… but there is no time to do this the gentle way!" Giovanni's voice was raised loudly but it didn't seem he was yelling in anger, more though of frustration. "You need to understand, even if I have to MAKE you understand."

"We're ready boss," Surge's voice called from outside the room.

"Bring it in," Giovanni stepped aside as Surge floated a Magneton into the room. The two disappeared behind Red's field of vision for a moment and all he could hear were mechanical clickings.

"What… What are you doing?" Red tried not to stammer or show fear.

"You broke my trust Red," Giovanni placed his hand on the boy's head, "And for that you must be punished; this is the only way you will learn not to defy me again."

The young trainer's red tinted eyes widened as Surge came back around with a controller of some kind in his hand and almost a grin on his face, "It's ready boss."

Without the slightest affliction Giovanni gave the command, "Do it."

Surge pressed the button and immediately the electric current from Magneton was focused through the machine and into Red. Sparks flew from the metal tie downs as Red screamed from the painful shock. It lasted only a few seconds and then everything went silent.

"Each of my generals will deal with you in their own _unique_ manner before you return to my care," Surge twisted a knob on the controller before pressing the button again. This time even greater current passed through the machine. The thunderous sound of electricity was deafening as red's body jumped and pulled at his binds on its own accord.

"I'll leave you to it then," Giovanni stepped out of the room leaving Red and Surge all alone.

Surge was quiet for a moment as he paced from side to side as if appraising the boy in bondage before him, "You really pissed the guy off brat; you know he not once told me I needed to take it easy on you?" Surge pressed the button and more shocks did come.

The electricity stopped again, "So you're supposed to be one of us, on our side now huh?" The retired lieutenant suddenly corrected his posture and adopted a very authoritative pose, probably left from his military days. His voice obviously deepened into a strict drill sergeant tone, "Do you know why you're here?" Surge leaned in close enough that he could feel the current flowing through Red's body, "Answer when a question is asked of you!" The button was pushed and shocks and screams resumed for another few vicious seconds, "You are now a member of Team Rocket!" More thunder and wails filled the room, "You will battle for our cause!" Every sentence was punctuated by another torturous press of the button by Surge, "You will carry out the mission of Team Rocket!" Tears stained Red's face as he tried to endure, barely even aware of the words being shouted into his face, "And you will not disobey your orders!"

The punishment, as it were, went on for over an hour. By the end of it, Red's wrists and ankles were worn raw from the involuntary pulls at the metal clasps which held him in place. His breath was ragged and quipped, as if his lungs were stuttering in their need for air.

The large man walked around the electrocution machine, as if admiring his handiwork, "I hope for your sake that you've learned your lesson now."

"I… th…" Red found himself unable to form words properly.

"Did I say we were done?" Surge warned him. He moved to the TV in front of Red, "The boss still wants you to watch, and now it's up to me to make sure you're watching." The TV turned on and was ready to play whatever propaganda had been lined up.

"And don't even think about sleeping through this!" Surge pulled a band out from over the electrocution hanger and placed it on Red's head. "Now you're in control of your own health. If you start looking off at other things or if your head droops forward because you're a little sleepy, then Magneton will shock you, like this!" He pushed Red's head forward causing the tie to pull and a shock was released through the machine. "You will look ahead and pay attention until the videos are over! Understood?"

Red didn't acknowledge Surge at all. He looked forward with his eyes unmoving, unblinking, focused just on breathing.

Surge grunted and left Red to his viewings.

It was only a few minutes in when Red's eyes began to wander the room and he moved his neck muscles just enough to trigger the band on his head and released the electric charge on himself. It stopped the moment he returned to a forward looking position. He managed only a few minor shocks for the first few hours. It seemed the longer his head was turned away from the screen the more severe of a shock he received.

Red was unsure what time it was, but it must have been late. The videos had been going for hours, and despite the shocks and their gruesome content his eyes were beginning to droop. His head began to nod forward but that caused another jolt from the machine he was attached to. He thought the videos couldn't go on for much longer, but they did. Hours turned in to all night, though it was hard to tell. The electrocutions became progressively worse as Red had a harder and harder time remaining alert and upright.

The adrenaline rush from the near constant electrocutions made it impossible to accurately tell time. The door eventually did open and Surge entered again. He wore a different set of clothes so Red was able to assume at least the night had passed.

"Magenton is running a little low on energy. We're going to have to find a way to fix this. In the mean time I suppose you should enjoy this little break. It won't last too long," Surge snickered as he disconnected the Magneton and floated it from the room.

Red waited for the man to leave and then his head fell forward. He was exhausted, frustrated, confused. In the midst of everything that had was going on, Red found himself wanting to cry. He shook it off and tried to remain positive, "It's okay… my friends will come soon, then everything will be alright."

Despite hanging in such an uncomfortable and awkward position, Red's head nodded forward and he dozed. Once a person has reached a certain stage of exhaustion it becomes impossible to retain any sense of time, or to have any recollection if one is dreaming or actually opening their eyes and seeing what really stands before them. For some unknown reason Red tilted his head skyward and made out the forms of two giants standing above him. One stood on four legs and the other on two, both gave off an aura of extraordinary power and they looked directly at him. After a moment the two looked to each other as each to confer amongst themselves.

A jolt to Red's senses jarred him back to reality as he found himself wet and cold. Surge stood before him holding an empty bucket of water pointed in his direction, "Good news, we found some better batteries that will save Magneton from wearing itself out now!" Surge spoke in his more traditional cocky swagger. He was wearing the same clothes Red remembered seeing on him the last time, which made it hard to tell if he had slept for several hours or just a few minutes.

Surge waved the remote in front of Red's face, "This time let's hear you say it."

Red looked up wearily at the man, "Say… what?"

Surge pressed the button and sent a horrible shock through Red's wet body, "You will address me as sir!" Red tried to remain defiant as Surge pressed the button again. The droplets were evaporating from Red's skin in small pockets of steam, "Now, what are you to address me as?" again Surge received no response and he pressed the button again.

Red's body gave several more painful spasms, "Sir!"

"Better," Surge grinned, "now who do you work for?" Again Red was quiet until Surge turned up the dial even further. Red screamed and dealt with the pain, unable to form the words in his mouth.

"We have a lot of work to do from the looks of it." Surge turned the dial up another notch, "Don't worry about me though, I could do this all day!"

Red refused to acknowledge the words Surge wanted from him. After several hours Surge affixed the band back to Red's head. "There are plenty of videos for you to watch still. You know how this goes. Have fun!"

Surge hit the play button and stepped out of the room again. Red's neck muscles could barely keep his face pointing straight anymore, but every time he let up his concentration just a bit he received the shock treatments. He wanted to collapse and sleep so bad, but it was impossible in this predicament. He knew he just had to endure the videos and then maybe things would level out. But hours went by and there was no sign of anything ending.

Everything began to blend together, and then it was an entire day that passed, and then two. The videos might have been repeating but Red could hardly tell. His mind couldn't focus and his memories were hazy. Three days. An additional three days of no food, no sleep, the inability to move, and near constant electrocutions, went by before the videos finally stopped.

Giovanni entered the room the moment after the screen turned black. He pulled the band from Red's head which cause the boy to jump as well as he could and look up at the man, but his eyes were empty. First the man pulled a handkerchief from his jack and wiped the tear stains from Red's face, then he pulled out the bottle of water and pressed it to the boy's lips. Some he drank, much of it was choked back out.

The shackles let go of Red's limbs and immediately the boy collapsed without their support. Giovanni caught Red and lifted him off the ground into his arms. He carried Red that way to another hospital like room where he was strapped down.

Though Red's body finally received some much needed sleep, rest did not come for him.

The next morning Red's senses awoke into overdrive as another pail of ice water was dumped over him. Red shouted and blinked the drowsiness from his eyes, "WHA…"

Giovanni stood at the foot of the bed, Koga beside him still holding the bucket. He finally noticed a numbing sensation spreading from his arm. He looked from his arm to the table nearby and noticed an empty syringe, "Wh…. Whaaa… wha…t… waaa…s… that…?" The effects from the previous several days had impaired his muscle control to speak properly.

Koga took the syringe, threw it in the bucket, and returned to Giovanni's side. "Don't worry about that," Giovanni assured him, "that was just something to keep you calm and open your mind a bit more."

Red's mouth hung agape as he breathed heavily, but he didn't have it in him to panic. Giovanni unstrapped the boy from the bed and sat him in a wheel chair. Red couldn't even ask where he was being taken.

The hallway was different from any he remembered the other day, not that his memory was functioning too well. Giovanni knocked on a door and Sabrina quickly opened it and stepped out. Red managed to look inside the room for a moment and saw at least five Hypnos and an Alakazam sitting in a circle and chanting something. In the center Red just made out Pika strapped to the floor, his eyes wide and dazed.

"Pi…k…" Red tried to call out. He pushed himself from the wheel chair though his body was a wreck of uncontrollable seizures. Koga was at Red's side in an instant and injected him with yet another syringe. A dizzy sensation immediately washed over Red's brain as he lost the will to do anything.

Giovanni continued his conversation with Sabrina, but Red couldn't comprehend anything that was being said. Sabrina bowed and returned to the room before Red felt he was being pushed further down the hall.

A large double door at the end of the hall led to a room padded with athletic mats, "I leave him in your hands," Giovanni told Koga before he turned and left the room. A beep and click signified the door locked behind him.

Koga said not a word as he pushed the chair into the room. He waited a moment in silence before he pushed the chair over and spilled Red harshly to the floor, "Oooafff!" Red groaned as he struggled to find the strength to push himself back up.

"Pathetic," Koga circled around the paralyzed boy, "Without your Pokémon you are incapable of nearly anything! You intend to serve Team Rocket like this?!"

"I...I…" Red tried to crawl away but Koga shoved him over onto his back and he was unable to move.

Koga turned and lit several incense candles in the room. The scents of the candles immediately filled the room. Red wasn't sure why, but after breathing in the strange smell he was overcome by strange emotions, a sense of hopelessness and fear. Red hadn't moved at all by the time Koga returned. Not at all gently, Koga grabbed one of Red's ankles and dragged him to the other side of the room. He pulled a Poké Ball from his belt and released a Tentacruel to a platform near the ceiling of the room. The Tentacruel reached a tentacle down as Koga offered it Red's ankle and the Pokémon hoisted the boy from the floor, upside down by his left leg.

"I spoke with Surge to find out how much of the video series you've seen," Koga turned the videos on and began to play them again. Red squeezed his eyes shut as hanging upside down was making his head ache, he hardly noticed as Koga moved another bucket of water directly underneath him. "Like Surge I expect you to pay close attention. This Tentacruel is very observant. And as its name implies, if it detects you not paying attention it will remedy the situation. Demonstration," As if commanded, the Tentacruel dropped Red's head into the bucket of water. The boy's arms waved and his body squirmed for several long seconds until Koga had him pulled him back from the bucket. Red's lungs forced him to cough and hack out the water he'd taken in.

"Now that you understand how this is going to proceed…" Koga pressed play and the propaganda began again. Koga pulled out another strange stick of incense and lit it at the front of the room, "Finish watching these clips, and think things over. You'll start to see things differently, I'm sure of it." Once it was lit Koga seemed to hurry from the room. He locked the door behind him as the scent in the room became overpowering. Despite not being able to move Red began to feel light and his vision multiplied. It was as if he were watching five TV screens that kept circling around each other.

While Red was still mesmerized by the strange sensations coursing through his body, he was abruptly dunked into the water and pulled back out, "I… I was…n't…" The Tentacruel seemed to hardly pay attention to Red and merely dunked him every few minutes at random. There was no telling when Red would find himself submerged. Sometimes Red found himself in the water even though he was paying attention to the videos. At least he thought he was paying attention to the videos. In any case, the situation made it impossible pass out much less sleep. Once again the fatigue that wracked Red's body left him unable to truly notice the passage of time, but it felt as though days had come and gone again.

The door to the room opened as Koga returned and stopped the videos, "The day is come. Do you know what today is?" Koga asked emotionlessly as he turned on the Television.

Red's condition left him hardly able to concentrate enough to pose intelligible responses to questions, "Mmm…m..ore… Vid…d…deos."

"No videos today. Today is quite the grand day in Kanto, so we're going to watch a live event," Koga changed the channel and on the TV was the opening ceremony for the Indigo League Championship.

The trainers who were participating in the tournament were all approaching the arena for their introductions. Most of the trainers Red had never heard of before, but then the cameras reached a face that halted Red's breathing, "If this next young man seems a little familiar well he should. This trainer from Pallet Town is a member of the famous Oak family. Blue Oak has been training hard for this day, effort that shows as he is the youngest participant of the event today. Might this young prodigy be ready to take the same crown once held by his father and grandfather?"

"Bl…Blue…" Red watched as the camera panned over the audience and he caught sight of many other familiar faces all there at the tournament. He was so focused on the events on the screen that he hardly felt Koga prick him with another syringe until it was already being put away.

Koga tried not to show his interest in Red recognizing a participant, "Do you know why you're in the predicament you're in?"

Red stared forward blankly for a moment before he turned and stared at Koga.

"No, this has very little to do with us," Koga grabbed Red's face tightly and directed his vision back to the screen, "Right there, those associates of yours who did nothing but lie to you and lead you astray, they are the true villains in this tale."

"T…th…that's not tr… true!" Red's voice cracked.

"But they are the ones who filled your head with lies with their version of what the world needs." Koga kneeled down to speak in lower, deeper tone, "It's not your fault you were caught up in this either. They are the ones who lied to you and told you the world was a good and safe place all the while they have allowed horrible things to happen to innocents everywhere!"

Red shook his head and stuttered, "B…but… my… f…friends…"

Koga tapped on the tentacle holding Red up and the boy's head was dropped into the bucket of water.

"Look!" Koga grabbed onto Red's face and held his eyes open towards the screen. Blue's first match was on, he was using his Golduck to trample over another trainer's Rapidash, "They aren't your friends, they don't care about you! They're not off looking for you, or about to come rescue you! You could be locked away in a dungeon for all eternity and they will continue on their merry happy lives just fine because they could care less!"

Red's eyes didn't move from the television set as Koga moved around him, "They told you the things they did so you wouldn't get in their way, so they could leave you behind." Tears welled up in Red's eyes. His emotions and thoughts were running rampant and no matter what he tried to tell himself he just couldn't reel them back under his control.

"Those… people… they are the true cause of all your pain!" Koga injected another drug into Red's back. Red's eyes shot open wide and then he screamed as it felt as though a fire was beginning to consume him.

"Those… people… they stole something from you. They stole the truth from you which was your right to know," The nerve agent Koga injected Red with made him think he was in terrible burning pain, but the tranquilizers kept him from moving his arms in any more than weak flops.

"Those… people… pushed you down a path of ruin!" Every sentence Koga spoke kept repeating over and over in Red's mind, "They intend to laugh as you burn!"

Red let out another cry, "N…no! They w…wouldn't!"

Koga had Red dunked in the bucket of water once again. Red continued to scream through the water. Koga pulled him back out and his body couldn't quite decide whether to breathe, cough, of scream even more.

"Those… people… were leading you to nothing but destruction and pain!" The tournament continued on over the air. Koga's words always became the harshest during one of Blue's battles. Red would be dunked every time he mentioned anything that sounded favorable about his friends. At least twice more Red was injected with some other chemical or drug; one moment he'd feel heavy and tired and unable to move, and the next a sudden blistering pain would wash over his entire body. The tournament was entering the semifinals, and blue was still in the running. "Those… people… have been laughing behind your back from the beginning!"

"W…wh…" Red's voice was horse from the last few hours of screams, and he still hadn't gotten over the stuttering caused by the electrical shocks, "…why… would th…they?"

A grin finally formed on Koga's form which he had to wipe from his features before he turned and lowered Red back to the ground, "Because, those people wouldn't be there enjoying themselves if it was a true friend who was missing. A true friend would have been tearing down the walls to recover their missing man. It's what Giovanni would do for any of us and certainly what I would do for him."

Red weakly looked up from the ground, "He… would…?"

"And he wants you as part of this family, yet you're the one who keeps denouncing his offers," Red's head sank to the floor and his body quivered as if he were crying.

Red watched until the end when Blue claimed the victory over his last opponent in the finals. Blue still didn't look at all impressed; he just turned and walked away from the arena. The announcers began their commentary, "It seems there was no one else in the tournament even capable of challenging Blue Oak today. He was definitely in top form, and has proven the Oak name is one that will continue to be taken seriously in the world of Pokémon battling."

Hurt and empty red tinged eyes did not blink as they attempted to focus at all of the Blues in through the hazy vision, "Why… Blue… why…?"

Another restless sleep fell over Red. He would leave and enter sleep in quick intervals as his mind tried to cope with everything that was happening. So many thoughts were jumbled together. Everything he had always thought was true was before was now questioned. Everything he thought was good and right with the world before started to look tainted and soiled. Still a part of him wanted to hold on.

Something startled Red into consciousness. He was unsure how long he'd been asleep, it could have an hour, or days even. But he was being carried. He realized it was Giovanni who had him in his arms and was carrying him down another hall. He said nothing as they approached a door which Sabrina opened for them.

Red wasn't even fully aware as Giovanni and Sabrina spoke to each other, "I'm counting on your particular brand of therapy. I need our ideals ingrained in his mind like second nature."

"Normal hypnosis will not provide the permanence you seek in this endeavor," Sabrina's voice as always was cold and near monotone.

"You have other methods," Giovanni insinuated strongly.

"Yes, but this one is strong of character," Sabrina placed a hand on Red's scalp. He flinched on contact but did not give any other reaction. "It could take much longer than a few days to instill the qualities you ask of me."

"Do what you can and keep me abreast of any progress," Giovanni sat Red down onto a chair inside the room.

"As you desire sir," Sabrina bowed and entered the room as well. The psychic girl opened a case which held six purple colored Poké Balls. From within them she called out several Abras and another Alakazam.

"I'm sure you're familiar with Giovani's videos," Sabrina stated as she pressed play on them yet again. "This time you're going to have some company watch them with you. These Abras are especially trained. They will monitor your thoughts and when you encounter a painful thought they will help you. Eventually the painful notions that exist in your mind about your past will become dimmer and dimmer until the belief is erased from your mind completely."

Red's eyes looked up at Sabrina but he said nothing.

Sabrina nodded, "You needn't fear, though this process is time consuming, your mind will feel much more at ease by the time we are completed."

All of the Abras sitting around Red opened their eyes, eerily in sync with each other, and stared into the boy's thoughts as the video played on. The first time his thoughts were attacked caused his eyes to open wide. It was painful in a way he'd never experienced before like a grating against his memories and his very self slowly filing it all away to a fine dust, ready to be blown away with the wind.

The mental tampering made the passage of time almost impossible to perceive. Days passed but the _therapy_ continued. Red's body entered bouts of micro sleep from being kept awake for so long.

Red pushed himself into a dark corner. Tears no longer fell from his eyes, but he buried his face into his knees. Sabrina approached him through the dark, "You sit here alone?"

"I am alone." Red responded instantly.

"What of your friends?" The question caused Red to cringe.

Crimson eyes looked up over Red's knees at Sabrina, "I have no _friends_."

A strange power behind Red's words cause Sabrina to take a step back, "…Do you have enemies?" Sabrina asked next.

"… _No._ " The reply was simple, stoic, but somehow aggressive.

Tempting another question, Sabrina pushed on, "Red… What is your mission?"

"I…" Red stared at Sabrina for a long moment, "I…" No other answer came. Red continued to stare at Sabrina unnervingly.

The connection between them was suddenly closed. Sabrina looked down to Red's sleeping face somewhat mystified as she separated her hand from the boy's forehead. He had somehow shut her out of his mind.

Giovanni heard Sabrina's clattering steps as she approached his office, "And how goes the process?" he asked without looking up.

"He is very extremely strong willed," Sabrina replied with only a hint of incredulity to her voice. "He somehow has enough control over his own mind to push the thoughts that cause pain aside and retain a thought pattern of neutrality which is impairing our ability to overwrite those thoughts."

"I see," Giovanni grinned for a moment, but it quickly faded away.

"Doubt has been firmly cemented in his mind regarding his past but there is still much uncertainty over his current perceptions," Sabrina looked down for a moment and contemplated her next words, "Further damage to his psyche could prove detrimental to his stability. Should this happen I cannot guarantee he would fully recover."

Giovanni sighed, "Thank you for your efforts."

Sabrina appeared to be considering whether or not to come forward and say more, "There's one other thing…"

"Oh?" Giovanni knew it rare for Sabrina to act nervous, even mildly so.

"There are areas within his mind…" Sabrina tried to find the right words to explain, "They are extremely well guarded, I've never seen this type of resistance in an adult with telepathic training much less in a child."

"What do you believe this means?" Giovanni asked curiously.

"I'm unsure," Sabrina tried to think, "Under other conditions I would have thought he possesses a psychic potential, but never has he exhibited any such tendencies… I believe there may be something greater at play within his mind."

Giovanni grinned, "He is exceptional, in every aspect of the word."

"Sir," Sabrina could somehow tell this news was not at all shocking to her leader, "how will you proceed with him now?"

"I will handle the next phase of his adaptation, there is no need to further concern yourself with the matter," Giovanni stated very matter of fact."

"I understand," Sabrina turned and left the room. Giovanni was not far behind her to collect the boy in question for the final adjustment.

Red's eyes slowly opened. He was still tired but something unusual was registering in his senses that was keeping him from simply falling back to sleep. It was then that he realized that he was comfortable. He finally noticed that he was on a very plush bed. The mattress was thick and foamy, a body could sink into it like a cloud, while the comforter above it was soft like feathery downs. The bed smelled good, like a musky cologne.

"You're finally awake," a deep voice spoke from the darkness. Red tried to push himself up and look around the room. He was still weak, but the sleep had done him good. Though dark the room he was in looked like a very modern home. Sitting at a large "C" desk not far from the bed was Giovanni himself.

"Was I…" Red's head was still groggy and he was having issues piecing together a question.

"You've been asleep here for almost two days. But you needed it, you're looking much better," Giovanni spoke as though nothing was wrong or unusual.

Red gripped onto the comforter he was on, "Where… am I?"

"You're in my quarters," Giovanni stood from his desk and approached the bed.

"Why?" Red was still weak but managed to push himself into a seating position.

"I needed to know for sure, if you've started to understand why we do the things we do," The room was very dim as Giovanni stood over Red and looked down at the boy. Once again it was a room with no windows, light was emanating from several computer monitors and dim lights built into the wall near the floor.

Red remained quiet, his facial expression yielded no change either.

"Sometimes…" Giovanni sighed and sat down on the edge of the bed beside Red, "Sometimes a decision must be made. Sometimes horrible decisions. Sometimes a few must die so that many may live. It's a terrible weight to be burdened with, but sometimes if someone doesn't make that choice then many will all perish."

"That…" Red was quiet for a moment as his mind worked through the words, "That makes sense."

Giovanni nodded, "Good, because it now falls to you to make that decision."

Red's eyes widened slightly and his mouth fell agape as he shook his head, "No, I can't decide something like that."

"I'm sorry," Giovanni's hand reached for Red's face and caressed his cheek, "but you have to."

"I won't," Red tried to show a brave face and remain defiant.

Giovanni stared into the boy's red eyes, "So this is where you've been hiding."

"What?" the words confused Red more than anything.

"You lack the proper motivation, but I promise you will have that," Giovanni put his hand against Red's bare chest and pushed him down onto his back.

"What are you doing?" Red asked as a sudden alarm sounded in his head.

Giovanni continued to stare down at Red. Part of him debated whether he could go through with it. His resolve solidified and his hand travelled down Red's body.

Red shivered from the touch and grabbed at Giovanni's hand, "No, don't touch me."

Giovanni shook his head, "This is how it must go." His hand reached the band of Red's underwear. Red's jaw quivered as he was unable to stop the stronger man from pulling his last bit of garb down and off his legs. He was exposed completely to the man's eyes.

"P…please…" Red whimpered weakly, "…don't..."

Red's pleas fell upon deaf ears. The room darkened to an almost pitch black. In the darkness Red's world alit in a terrible pain. The night failed to end quickly, and before it was over Red was forced to confront a betrayal by his own body.

By the time the act concluded, Red was left with nothing but confusion. His mental walls finally collapsed and he began to bawl like a small child. Red huddled helpless in the corner of his mind as his world shattered. It was so dark and suddenly nothing made sense anymore. Who he was, what he had been, what had been going on, what he wanted out of life, his goals and dreams were smashed to bits leaving him very alone.

Giovanni pulled the covers over them both and Red continued to cry as loud as his lungs allowed for a long time. There were no more struggles from the boy, and so Giovanni cradled him in his arms through the entire emotional bout. Once Red began to calm and only a minor bout of hyperventilation remained, Giovanni leaned in closer to kiss Red on the cheek.

"I know you feel destroyed right now Red, but I promise you I will be here for you… I promise you that I will fix you…" He turned the boy around to stare deep into the dark red empty eyes, "because I love you." His lips ghosted over the boys in a slow feathered kiss. He pulled the boy's head to his shoulder and held him close until Red fell asleep.

* * *

 **End Chapter**

I put Red through so much hell. I really feel bad for it. I researched some actual torture methods to make it seem a little more realistic with some universe twists involved. That may have also made this chapter a little intense. Hope you enjoyed it and please leave some feedback.

Thanks!


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